General information for g3426.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine-protein kinase receptor torso.
Parent gene
- The parent gene g3426 is located on chr_3: 25310522..25314308 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g3426 | g3426.t1 | TSS | g3426.t1 | 25310156 | 25310156 |
| chr_3 | g3426 | g3426.t1 | isoform | g3426.t1 | 25310522 | 25314308 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon1 | 25310522 | 25310683 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS1 | 25310522 | 25310683 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon2 | 25310743 | 25310973 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS2 | 25310743 | 25310973 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon3 | 25311061 | 25311714 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS3 | 25311061 | 25311714 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon4 | 25312236 | 25312707 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS4 | 25312236 | 25312707 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon5 | 25312779 | 25312950 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS5 | 25312779 | 25312950 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon6 | 25313169 | 25313672 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS6 | 25313169 | 25313672 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon7 | 25313731 | 25313850 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS7 | 25313731 | 25313850 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon8 | 25313931 | 25314224 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS8 | 25313931 | 25314224 |
| chr_3 | g3426 | g3426.t1 | exon | g3426.t1.exon9 | 25314284 | 25314308 |
| chr_3 | g3426 | g3426.t1 | cds | g3426.t1.CDS9 | 25314284 | 25314308 |
| chr_3 | g3426 | g3426.t1 | TTS | g3426.t1 | 25314603 | 25314603 |
Sequences
>g3426.t1 Gene=g3426 Length=2634
ATGGGAGTTTTAGTGATAAAATATGTACAGCTTATTTGTGTGGCATTTTTTGTGAAAAAT
TCAAATTGTGCTCCTATTGATAAAGAAGTAGCATCGCATTTGAAAATTTCTGCATGTATA
GCAGAATGTTTAAATGTCAATCGATACAGTAATAATTCAAAAGTATTGGAAAATTGCATG
AATGACTGCTCAGAAGCAAATGATCGTATTTTAAATTATGAAGCTCTAGCTGAAAGCTCA
AATTTTTCTCTCTATTGTCGCGATACTCAATCGTTATTAATAAAAATTGACCACGAGGTT
TCAGAGGCGGCGGTTGATAAGAATGAGACATTTGTCTACATGCTCAAGGTTAAGGAGTCG
ACTGGAAAATTTACTGATCGCATTTACTCATTCTCTGATGAGAGTTTGATTAATGTCACT
ATTCATGACCCAAGCTTAGCTGAGACGACGACACTCTCGTATGAAATTACGGCATATATT
ATATCATCAAAAAATTCCACTGTGCAGATGTTAGGAAAAAAGAATTTTACAACATTAATG
CCTGACTTTAAGCCTGAACCTGTGACTGAAGATATGATTTTTGACTTAAAATGGATTGAG
TATTTTAACAAAACTGAAAATGATCAACGGTTAAATCTCACGTTTAAATGGTTGCCAGAA
AGATCTCATACATGTTATTATAATGTATTGTTTTACGGAAGCACATCAATTGATTCTTTA
GACATTGAATCATATCCTGTTCCTATTGGAAAACTCTATGAATATACAATGAGTAATTTA
AGATACGATTCTGAATATTATGTTGCAATTCGTGCTGTCAATAAAAACAAACCTGATCTT
TATAGCCAAGTTCAATGGAAAGAAATTTCTTCACCAGAAAATGAAAATAAGTTTGAAATC
AAGACGACATTGAAGCATGTTAGTGACAACAATTTCGATGTAAAAATAACATGGAATGAG
CCAAGCACATTGCCCAATTATTATCGAGTTGAATTAAAAAATTTACATGCTCACACACGA
AAGGATTATACAGCTGATGTCAAAGGAACAGAAAAGTTTTATTTATTTAAAAACATCGAA
TTAACAAGCTTAAATATTTTTATCAACGTCACTGGTTTTGGTCCAAGCAACAATATTCAT
GTACATGACTATGCTTTCATCAATAGGCAAATAATCCCTCAAAGCAAAGTCATCAACATT
CTCTTCTACATTTTTGTTGCACTTGTCGTTATTCTATTTCTATTTCTCTTCAAAGTTTGG
AAAGGTCGAATTGACTCGTTCATTTCAATTTTTGCACAGAAGCGAATTGATGATTTGGAT
ATTGAAATTGTGAAGACAATGTCAACAGGAACAGTCTTGGATGCAATTGCTGAGTTGACG
AAAGATGAGAAAATGGAAATTGAAAGGGAAAATATCACAGTACTGCAGTTAATTGGTGAA
GGCGCTTTTGGACTTGTAAAGAAAGGTCTGATAATAAAGAATGGTGAAAAGCAGTATGTC
GCTGTCAAAATGATCAAAAACACATCAAATCTAGAGGATATAAAGCAATTTCATCAGGAG
ATAAGTGTCATGAAGTCAGTTGGACAACATGAGAACATTGTTAGCATAGTTGGTCATTGC
ACTTCTGATATCAATGAGTTGATGTTGCTGACAGAATATTGTGATGACGGAAGTTTACTT
GATCTTTTGAGACTTGAGTTTGCAAAGCAATTTAAGTTTTATGATACGAAAGGAAAGTTA
AATGCGTCAGTGCAGATTACGATGGAAAAGTATTCGGACAGCTTGTTGAACTTTGACATG
TCAGAAAGAGACAAGAAAGAAATTTCATATAAAAATATCGGTTGTTCAGCAACTCCAACT
GCATTTAAAAATAACAAGCTTTTTGTAGTAAACCAAATGTATGATGAGCTGAATAATAAC
ATTAAAAATGAATCATTTTTAAAAGCAATTGAAATGACAGCAACAAATGCACTTTATCTT
AAATTAAATGAACAAGACACACAAACTACAAACATTATCATTGATGAAGAAGATTCTGTG
ATTGAATTTTTGACTTCAAGCGATCTTCTTTCATTTGCAAAACAAATTTGTGATGGCATG
GACTTTTTAGCAAGGAAAAAAGTTGTCCATCGTGATTTAGCTGCGAGAAACATTCTCGTT
TGTTCAAACAAAACTGTCAAAATTTCTGATTTTGGCTTGAGTCGTGACATTTATCAGGAC
CTTGTCTATAGAAAAACAGGAAATGGAAAATTGCCAATTAAATGGCTCGCACTAGAATCG
ATGACACACCAAGTCTATACCTCGCAAAGTGATGTATGGTCCTTTGGTGTGCTTCTTTAT
GAAATTGTAACACTTGGATGTGTTCCGTATTCATCGATAAATGTTGAAAATTTATTGAAA
TTCCTAAGATCAGGTTTTCGCATGGAACGACCAAGTCATTGCCATATATTACTATACGAG
CTGATGATGCTATGCTGGCATGCAAATCCTATGAATCGACCCTCCTTCGATGAGCTGTCA
TTGAAATTAAATGAATTCTTGCTCATGGAAAATTGGGGTGAACGAATTATTGATTTATCC
AAGATGTTCACTAAATGTATGAACGATGTGAATTACATGAAGCCATTAATCTGA
>g3426.t1 Gene=g3426 Length=877
MGVLVIKYVQLICVAFFVKNSNCAPIDKEVASHLKISACIAECLNVNRYSNNSKVLENCM
NDCSEANDRILNYEALAESSNFSLYCRDTQSLLIKIDHEVSEAAVDKNETFVYMLKVKES
TGKFTDRIYSFSDESLINVTIHDPSLAETTTLSYEITAYIISSKNSTVQMLGKKNFTTLM
PDFKPEPVTEDMIFDLKWIEYFNKTENDQRLNLTFKWLPERSHTCYYNVLFYGSTSIDSL
DIESYPVPIGKLYEYTMSNLRYDSEYYVAIRAVNKNKPDLYSQVQWKEISSPENENKFEI
KTTLKHVSDNNFDVKITWNEPSTLPNYYRVELKNLHAHTRKDYTADVKGTEKFYLFKNIE
LTSLNIFINVTGFGPSNNIHVHDYAFINRQIIPQSKVINILFYIFVALVVILFLFLFKVW
KGRIDSFISIFAQKRIDDLDIEIVKTMSTGTVLDAIAELTKDEKMEIERENITVLQLIGE
GAFGLVKKGLIIKNGEKQYVAVKMIKNTSNLEDIKQFHQEISVMKSVGQHENIVSIVGHC
TSDINELMLLTEYCDDGSLLDLLRLEFAKQFKFYDTKGKLNASVQITMEKYSDSLLNFDM
SERDKKEISYKNIGCSATPTAFKNNKLFVVNQMYDELNNNIKNESFLKAIEMTATNALYL
KLNEQDTQTTNIIIDEEDSVIEFLTSSDLLSFAKQICDGMDFLARKKVVHRDLAARNILV
CSNKTVKISDFGLSRDIYQDLVYRKTGNGKLPIKWLALESMTHQVYTSQSDVWSFGVLLY
EIVTLGCVPYSSINVENLLKFLRSGFRMERPSHCHILLYELMMLCWHANPMNRPSFDELS
LKLNEFLLMENWGERIIDLSKMFTKCMNDVNYMKPLI
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g3426.t1 | CDD | cd00192 | PTKc | 478 | 843 | 7.44841E-109 |
| 9 | g3426.t1 | Coils | Coil | Coil | 56 | 76 | - |
| 7 | g3426.t1 | Gene3D | G3DSA:3.30.200.20 | Phosphorylase Kinase; domain 1 | 432 | 554 | 2.3E-27 |
| 8 | g3426.t1 | Gene3D | G3DSA:1.10.510.10 | Transferase(Phosphotransferase) domain 1 | 652 | 850 | 5.8E-54 |
| 2 | g3426.t1 | PANTHER | PTHR24416:SF340 | TYROSINE-PROTEIN KINASE RECEPTOR TORSO | 189 | 845 | 2.8E-98 |
| 3 | g3426.t1 | PANTHER | PTHR24416 | TYROSINE-PROTEIN KINASE RECEPTOR | 189 | 845 | 2.8E-98 |
| 14 | g3426.t1 | PIRSF | PIRSF000615 | TyrPK_CSF1-R | 42 | 178 | 2.1 |
| 13 | g3426.t1 | PIRSF | PIRSF000615 | TyrPK_CSF1-R | 345 | 870 | 2.4E-89 |
| 1 | g3426.t1 | Pfam | PF07714 | Protein tyrosine and serine/threonine kinase | 473 | 842 | 9.3E-88 |
| 11 | g3426.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 399 | - |
| 12 | g3426.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 400 | 420 | - |
| 10 | g3426.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 421 | 877 | - |
| 19 | g3426.t1 | ProSitePatterns | PS00107 | Protein kinases ATP-binding region signature. | 478 | 503 | - |
| 18 | g3426.t1 | ProSitePatterns | PS00109 | Tyrosine protein kinases specific active-site signature. | 708 | 720 | - |
| 20 | g3426.t1 | ProSiteProfiles | PS50011 | Protein kinase domain profile. | 472 | 847 | 38.577 |
| 17 | g3426.t1 | SMART | SM00219 | tyrkin_6 | 472 | 843 | 4.3E-116 |
| 4 | g3426.t1 | SUPERFAMILY | SSF49265 | Fibronectin type III | 216 | 358 | 3.63E-5 |
| 5 | g3426.t1 | SUPERFAMILY | SSF56112 | Protein kinase-like (PK-like) | 459 | 839 | 2.59E-73 |
| 6 | g3426.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 23 | - |
| 16 | g3426.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 398 | 420 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0004713 | protein tyrosine kinase activity | MF |
| GO:0005524 | ATP binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0004672 | protein kinase activity | MF |
| GO:0006468 | protein phosphorylation | BP |
KEGG
Orthology
- This transcript has been annotated with K12378 (tyrosine-protein kinase receptor torso)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
